Functional dyspepsia is a disease, in which there is no organic lesion but chronic and repetitive postprandial fullness, early satiation, epigastric pain, and epigastric burning. Functional dyspepsia is not life-threatening but its symptoms are relapsing and remitting and persist over a lifetime, limiting the social life and reducing the quality of life. Therefore, the treatment for acute relapsing period may help improve the short-term symptoms. Continuous medication may be needed to improve the long-term symptoms. Research designs to demonstrate the short-term efficacy of therapeutic agents may differ from clinical trials to demonstrate long-term efficacy. There are many difficulties in clinical trial design, implementation, and screening because there are no international standards of clinical trials for functional dyspepsia. The purpose of this guideline recommendation is to develop a standard for clinical trials, such as clinical trial subjects and evaluation methods, in the development of therapeutic agents for functional dyspepsia. The ultimate aim is to enhance the safety and efficacy of therapeutic agents for functional dyspepsia and promote the development of new therapeutic agents. (Korean J Gastroenterol 2018;72:170-178)